Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection
For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669577/ https://www.ncbi.nlm.nih.gov/pubmed/26645052 http://dx.doi.org/10.1016/j.pvr.2015.05.004 |
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author | Cullen, Michael Boland, Joseph F. Schiffman, Mark Zhang, Xijun Wentzensen, Nicolas Yang, Qi Chen, Zigui Yu, Kai Mitchell, Jason Roberson, David Bass, Sara Burdette, Laurie Machado, Moara Ravichandran, Sarangan Luke, Brian Machiela, Mitchell J. Andersen, Mark Osentoski, Matt Laptewicz, Michael Wacholder, Sholom Feldman, Ashlie Raine-Bennett, Tina Lorey, Thomas Castle, Philip E. Yeager, Meredith Burk, Robert D. Mirabello, Lisa |
author_facet | Cullen, Michael Boland, Joseph F. Schiffman, Mark Zhang, Xijun Wentzensen, Nicolas Yang, Qi Chen, Zigui Yu, Kai Mitchell, Jason Roberson, David Bass, Sara Burdette, Laurie Machado, Moara Ravichandran, Sarangan Luke, Brian Machiela, Mitchell J. Andersen, Mark Osentoski, Matt Laptewicz, Michael Wacholder, Sholom Feldman, Ashlie Raine-Bennett, Tina Lorey, Thomas Castle, Philip E. Yeager, Meredith Burk, Robert D. Mirabello, Lisa |
author_sort | Cullen, Michael |
collection | PubMed |
description | For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV-related cancers. To permit the large-scale study of HPV genome variability and precancer/cancer, starting with HPV16 and cervical cancer, we developed a high-throughput next-generation sequencing (NGS) whole-genome method. We designed a custom HPV16 AmpliSeq™ panel that generated 47 overlapping amplicons covering 99% of the genome sequenced on the Ion Torrent Proton platform. After validating with Sanger, the current “gold standard” of sequencing, in 89 specimens with concordance of 99.9%, we used our NGS method and custom annotation pipeline to sequence 796 HPV16-positive exfoliated cervical cell specimens. The median completion rate per sample was 98.0%. Our method enabled us to discover novel SNPs, large contiguous deletions suggestive of viral integration (OR of 27.3, 95% CI 3.3–222, P=0.002), and the sensitive detection of variant lineage coinfections. This method represents an innovative high-throughput, ultra-deep coverage technique for HPV genomic sequencing, which, in turn, enables the investigation of the role of genetic variation in HPV epidemiology and carcinogenesis. |
format | Online Article Text |
id | pubmed-4669577 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-46695772016-12-01 Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection Cullen, Michael Boland, Joseph F. Schiffman, Mark Zhang, Xijun Wentzensen, Nicolas Yang, Qi Chen, Zigui Yu, Kai Mitchell, Jason Roberson, David Bass, Sara Burdette, Laurie Machado, Moara Ravichandran, Sarangan Luke, Brian Machiela, Mitchell J. Andersen, Mark Osentoski, Matt Laptewicz, Michael Wacholder, Sholom Feldman, Ashlie Raine-Bennett, Tina Lorey, Thomas Castle, Philip E. Yeager, Meredith Burk, Robert D. Mirabello, Lisa Papillomavirus Res Article For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV-related cancers. To permit the large-scale study of HPV genome variability and precancer/cancer, starting with HPV16 and cervical cancer, we developed a high-throughput next-generation sequencing (NGS) whole-genome method. We designed a custom HPV16 AmpliSeq™ panel that generated 47 overlapping amplicons covering 99% of the genome sequenced on the Ion Torrent Proton platform. After validating with Sanger, the current “gold standard” of sequencing, in 89 specimens with concordance of 99.9%, we used our NGS method and custom annotation pipeline to sequence 796 HPV16-positive exfoliated cervical cell specimens. The median completion rate per sample was 98.0%. Our method enabled us to discover novel SNPs, large contiguous deletions suggestive of viral integration (OR of 27.3, 95% CI 3.3–222, P=0.002), and the sensitive detection of variant lineage coinfections. This method represents an innovative high-throughput, ultra-deep coverage technique for HPV genomic sequencing, which, in turn, enables the investigation of the role of genetic variation in HPV epidemiology and carcinogenesis. Elsevier 2015-06-15 /pmc/articles/PMC4669577/ /pubmed/26645052 http://dx.doi.org/10.1016/j.pvr.2015.05.004 Text en http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Cullen, Michael Boland, Joseph F. Schiffman, Mark Zhang, Xijun Wentzensen, Nicolas Yang, Qi Chen, Zigui Yu, Kai Mitchell, Jason Roberson, David Bass, Sara Burdette, Laurie Machado, Moara Ravichandran, Sarangan Luke, Brian Machiela, Mitchell J. Andersen, Mark Osentoski, Matt Laptewicz, Michael Wacholder, Sholom Feldman, Ashlie Raine-Bennett, Tina Lorey, Thomas Castle, Philip E. Yeager, Meredith Burk, Robert D. Mirabello, Lisa Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
title | Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
title_full | Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
title_fullStr | Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
title_full_unstemmed | Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
title_short | Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection |
title_sort | deep sequencing of hpv16 genomes: a new high-throughput tool for exploring the carcinogenicity and natural history of hpv16 infection |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669577/ https://www.ncbi.nlm.nih.gov/pubmed/26645052 http://dx.doi.org/10.1016/j.pvr.2015.05.004 |
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